Protein Modeling C

[Phenylethylamine]

The page http://cbm.msoe.edu/includes/pdf/SO/201 ... iption.pdf which is the on-site description this year says so. So either I found something you didn't know, or I'm dumb. I'm guessing the latter as you seem to be an expert in this event.

Ah, I see. My guess would be that whoever created that description did so by copy-pasting last year's and changing the files at the top, and they probably missed that paragraph. You're not dumb; someone at the CBM was just a little careless.

[gigaboo]

The page http://cbm.msoe.edu/includes/pdf/SO/201 ... iption.pdf which is the on-site description this year says so. So either I found something you didn't know, or I'm dumb. I'm guessing the latter as you seem to be an expert in this event.

Ah, I see. My guess would be that whoever created that description did so by copy-pasting last year's and changing the files at the top, and they probably missed that paragraph. You're not dumb; someone at the CBM was just a little careless.

I'm assuming you did this event last year, so that means that the whole thing about the flu is not important, right? We only need to know protein-ish stuff from this year's proteins, correct?

[Phenylethylamine]

The page http://cbm.msoe.edu/includes/pdf/SO/201 ... iption.pdf which is the on-site description this year says so. So either I found something you didn't know, or I'm dumb. I'm guessing the latter as you seem to be an expert in this event.

Ah, I see. My guess would be that whoever created that description did so by copy-pasting last year's and changing the files at the top, and they probably missed that paragraph. You're not dumb; someone at the CBM was just a little careless.

I'm assuming you did this event last year, so that means that the whole thing about the flu is not important, right? We only need to know protein-ish stuff from this year's proteins, correct?

Yes, I did the event last year; last year's protein was influenza hemagglutinin, which is where the mention of the flu came from. But the event has nothing to do with the flu this year, so you're right, you only need to know stuff about this year's proteins and induced pluripotent stem cells.

[Mithrandir]

If you look at the scoring guide last year you get points for representing which parts are beta pleated sheets and alpha helixes. You get no additional points for color coding them if you already have them folded in the correct way. The only advantage is that if you color code them then you don't have to worry about you secondary structures being shaped correctly.

Even if you color code your secondary structures, the judges will still want to see that they are folded correctly. Color coding could be a backup in case some of your secondary structures get a little bent out of shape, but it cannot replace correct folding.

Yes you're right. I double checked the scoring guide. You used to have the option of color coding, but now you have to shape the secondary structures for the maximum number of points.

[gigaboo]

Is 483 included? When I use Jmol, it appears as if only 399-482 are parts of it. Is my file corrupted? What do I not understand? The 2wbu file only has 84 in the chain, so I am officially confused.

[Phenylethylamine]

Is 483 included? When I use Jmol, it appears as if only 399-482 are parts of it. Is my file corrupted? What do I not understand? The 2wbu file only has 84 in the chain, so I am officially confused.

Yes, 483 should be included, and the chain should be 85 residues in length. What viewing mode are you using? It's possible there's something wrong with your PDB file- in which case I suppose you could try re-downloading it- but it's much more likely that you somehow inadvertently hid residue 483 (not to disparage your Jmol skills; it can be a fairly easy thing to do without meaning to). Unless you opened the PDB file in a text editor and deleted something, it's hard to see how the file itself could be corrupt.

[nanowhale]

Where should I put the crosslinkers on the protein? That is something that I have been wondering about. (my regionals are this Saturday)

[EastStroudsburg13]

The cross linkers are meant to stabilize your model. They don't have to have anything to do with the function of the protein. Just pick some spots on your protein that seem like good spots to use the linkers. I used three of mine on the three sets of beta sheets, and the other three went on the other side of the zinc fingers, but you can put yours where you want them.

[Phenylethylamine]

The cross linkers are meant to stabilize your model. They don't have to have anything to do with the function of the protein. Just pick some spots on your protein that seem like good spots to use the linkers. I used three of mine on the three sets of beta sheets, and the other three went on the other side of the zinc fingers, but you can put yours where you want them.

In fact, you don't even have to use any of them if you don't want to.

I'm considering dissecting them and using them as the tops of my vertical support posts so the whole protein is removable from its supports (but still stays pretty firmly attached on its own), which might be useful to the judges when they have to look at it from various sides.

[Megan95]

I was wondering... on the Jmol of 2wbu, what are the red sphere things? Are they hydrogen molecules or something? I looked up the structure and found the alpha helixes and sidechains, but I just can't figure out what the little spheres are.

When you first open a file in Jmol, it shows you all the atoms of the protein in "ball-and-stick" format. The spheres are individual atoms; red ones are oxygen in the default color scheme.

Have you been using the menus in Jmol or the command prompt? (That is, have you been changing the way you view the molecule at all, and if so, how?)

For anyone new to the event, I recommend reading the Protein Modeling Wiki; if you have more questions after reading that (which you most probably will), come back and ask (this also helps us keep updating the wiki to make it as helpful as possible).

I've been using the menus to try to figure out what those (the molecules) are and which creative additions to add. I still don't really understand Jmol, so I'm trying to avoid messing around and confusing myself further, and we don't have our mini-toobers yet, so I can't really do much now, but I'm trying to start with figuring out the sidechains.